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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.6

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-03-08, 11:35 based on data in: /gpfs/data/cbc/dspade/EGME/data/qc


        General Statistics

        Showing 195/195 rows and 5/6 columns.
        Sample Name% Aligned% Dups% GCLengthM Seqs
        Library_01
        93.1%
        52%
        29 bp
        13.7
        Library_01_mRNA_mapped_sorted
        100%
        Library_01_miRNA_mapped_sorted
        100%
        Library_01_piRNA_mapped_sorted
        100%
        Library_01_tRNA_mapped_sorted
        100%
        Library_02
        94.9%
        54%
        27 bp
        21.7
        Library_02_mRNA_mapped_sorted
        100%
        Library_02_miRNA_mapped_sorted
        100%
        Library_02_piRNA_mapped_sorted
        100%
        Library_02_tRNA_mapped_sorted
        100%
        Library_03
        93.0%
        53%
        27 bp
        12.8
        Library_03_mRNA_mapped_sorted
        100%
        Library_03_miRNA_mapped_sorted
        100%
        Library_03_piRNA_mapped_sorted
        100%
        Library_03_tRNA_mapped_sorted
        100%
        Library_04
        92.0%
        52%
        28 bp
        22.8
        Library_04_mRNA_mapped_sorted
        100%
        Library_04_miRNA_mapped_sorted
        100%
        Library_04_piRNA_mapped_sorted
        100%
        Library_04_tRNA_mapped_sorted
        100%
        Library_05
        90.2%
        55%
        27 bp
        17.3
        Library_05_mRNA_mapped_sorted
        100%
        Library_05_miRNA_mapped_sorted
        100%
        Library_05_piRNA_mapped_sorted
        100%
        Library_05_tRNA_mapped_sorted
        100%
        Library_06
        93.1%
        61%
        38 bp
        13.8
        Library_06_mRNA_mapped_sorted
        100%
        Library_06_miRNA_mapped_sorted
        100%
        Library_06_piRNA_mapped_sorted
        100%
        Library_06_tRNA_mapped_sorted
        100%
        Library_07
        88.3%
        61%
        33 bp
        16.6
        Library_07_mRNA_mapped_sorted
        100%
        Library_07_miRNA_mapped_sorted
        100%
        Library_07_piRNA_mapped_sorted
        100%
        Library_07_tRNA_mapped_sorted
        100%
        Library_08
        91.7%
        58%
        32 bp
        16.3
        Library_08_mRNA_mapped_sorted
        100%
        Library_08_miRNA_mapped_sorted
        100%
        Library_08_piRNA_mapped_sorted
        100%
        Library_08_tRNA_mapped_sorted
        100%
        Library_09
        92.5%
        52%
        28 bp
        20.0
        Library_09_mRNA_mapped_sorted
        100%
        Library_09_miRNA_mapped_sorted
        100%
        Library_09_piRNA_mapped_sorted
        100%
        Library_09_tRNA_mapped_sorted
        100%
        Library_10
        94.1%
        53%
        27 bp
        15.1
        Library_10_mRNA_mapped_sorted
        100%
        Library_10_miRNA_mapped_sorted
        100%
        Library_10_piRNA_mapped_sorted
        100%
        Library_10_tRNA_mapped_sorted
        100%
        Library_11
        94.1%
        58%
        34 bp
        17.2
        Library_11_mRNA_mapped_sorted
        100%
        Library_11_miRNA_mapped_sorted
        100%
        Library_11_piRNA_mapped_sorted
        100%
        Library_11_tRNA_mapped_sorted
        100%
        Library_12
        91.7%
        55%
        29 bp
        14.6
        Library_12_mRNA_mapped_sorted
        100%
        Library_12_miRNA_mapped_sorted
        100%
        Library_12_piRNA_mapped_sorted
        100%
        Library_12_tRNA_mapped_sorted
        100%
        Library_13
        89.1%
        48%
        39 bp
        10.5
        Library_13_mRNA_mapped_sorted
        100%
        Library_13_miRNA_mapped_sorted
        100%
        Library_13_piRNA_mapped_sorted
        100%
        Library_13_tRNA_mapped_sorted
        100%
        Library_14
        91.4%
        57%
        29 bp
        17.0
        Library_14_mRNA_mapped_sorted
        100%
        Library_14_miRNA_mapped_sorted
        100%
        Library_14_piRNA_mapped_sorted
        100%
        Library_14_tRNA_mapped_sorted
        100%
        Library_15
        91.4%
        58%
        34 bp
        26.7
        Library_15_mRNA_mapped_sorted
        100%
        Library_15_miRNA_mapped_sorted
        100%
        Library_15_piRNA_mapped_sorted
        100%
        Library_15_tRNA_mapped_sorted
        100%
        Library_16
        90.9%
        54%
        29 bp
        16.8
        Library_16_mRNA_mapped_sorted
        100%
        Library_16_miRNA_mapped_sorted
        100%
        Library_16_piRNA_mapped_sorted
        100%
        Library_16_tRNA_mapped_sorted
        100%
        Library_17
        92.8%
        53%
        32 bp
        21.4
        Library_17_mRNA_mapped_sorted
        100%
        Library_17_miRNA_mapped_sorted
        100%
        Library_17_piRNA_mapped_sorted
        100%
        Library_17_tRNA_mapped_sorted
        100%
        Library_18
        91.2%
        53%
        29 bp
        12.5
        Library_18_mRNA_mapped_sorted
        100%
        Library_18_miRNA_mapped_sorted
        100%
        Library_18_piRNA_mapped_sorted
        100%
        Library_18_tRNA_mapped_sorted
        100%
        Library_19
        93.4%
        54%
        29 bp
        16.8
        Library_19_mRNA_mapped_sorted
        100%
        Library_19_miRNA_mapped_sorted
        100%
        Library_19_piRNA_mapped_sorted
        100%
        Library_19_tRNA_mapped_sorted
        100%
        Library_20
        89.4%
        54%
        29 bp
        5.8
        Library_20_mRNA_mapped_sorted
        100%
        Library_20_miRNA_mapped_sorted
        100%
        Library_20_piRNA_mapped_sorted
        100%
        Library_20_tRNA_mapped_sorted
        100%
        Library_21
        92.1%
        55%
        30 bp
        20.1
        Library_21_mRNA_mapped_sorted
        100%
        Library_21_miRNA_mapped_sorted
        100%
        Library_21_piRNA_mapped_sorted
        100%
        Library_21_tRNA_mapped_sorted
        100%
        Library_22
        87.8%
        59%
        29 bp
        22.4
        Library_22_mRNA_mapped_sorted
        100%
        Library_22_miRNA_mapped_sorted
        100%
        Library_22_piRNA_mapped_sorted
        100%
        Library_22_tRNA_mapped_sorted
        100%
        Library_23
        89.2%
        63%
        29 bp
        4.0
        Library_23_mRNA_mapped_sorted
        100%
        Library_23_miRNA_mapped_sorted
        100%
        Library_23_piRNA_mapped_sorted
        100%
        Library_23_tRNA_mapped_sorted
        100%
        Library_24
        85.5%
        57%
        25 bp
        1.0
        Library_24_mRNA_mapped_sorted
        100%
        Library_24_miRNA_mapped_sorted
        100%
        Library_24_piRNA_mapped_sorted
        100%
        Library_24_tRNA_mapped_sorted
        100%
        Library_25
        89.4%
        50%
        38 bp
        16.5
        Library_25_mRNA_mapped_sorted
        100%
        Library_25_miRNA_mapped_sorted
        100%
        Library_25_piRNA_mapped_sorted
        100%
        Library_25_tRNA_mapped_sorted
        100%
        Library_26
        91.2%
        57%
        32 bp
        8.4
        Library_26_mRNA_mapped_sorted
        100%
        Library_26_miRNA_mapped_sorted
        100%
        Library_26_piRNA_mapped_sorted
        100%
        Library_26_tRNA_mapped_sorted
        100%
        Library_27
        91.8%
        53%
        29 bp
        20.3
        Library_27_mRNA_mapped_sorted
        100%
        Library_27_miRNA_mapped_sorted
        100%
        Library_27_piRNA_mapped_sorted
        100%
        Library_27_tRNA_mapped_sorted
        100%
        Library_28
        91.8%
        52%
        35 bp
        25.8
        Library_28_mRNA_mapped_sorted
        100%
        Library_28_miRNA_mapped_sorted
        100%
        Library_28_piRNA_mapped_sorted
        100%
        Library_28_tRNA_mapped_sorted
        100%
        Library_29
        91.6%
        55%
        32 bp
        32.7
        Library_29_mRNA_mapped_sorted
        100%
        Library_29_miRNA_mapped_sorted
        100%
        Library_29_piRNA_mapped_sorted
        100%
        Library_29_tRNA_mapped_sorted
        100%
        Library_30
        90.7%
        53%
        28 bp
        14.9
        Library_30_mRNA_mapped_sorted
        100%
        Library_30_miRNA_mapped_sorted
        100%
        Library_30_piRNA_mapped_sorted
        100%
        Library_30_tRNA_mapped_sorted
        100%
        Library_31
        90.9%
        58%
        31 bp
        12.0
        Library_31_mRNA_mapped_sorted
        100%
        Library_31_miRNA_mapped_sorted
        100%
        Library_31_piRNA_mapped_sorted
        100%
        Library_31_tRNA_mapped_sorted
        100%
        Library_32
        91.3%
        60%
        29 bp
        25.1
        Library_32_mRNA_mapped_sorted
        100%
        Library_32_miRNA_mapped_sorted
        100%
        Library_32_piRNA_mapped_sorted
        100%
        Library_32_tRNA_mapped_sorted
        100%
        Library_33
        83.2%
        57%
        27 bp
        1.6
        Library_33_mRNA_mapped_sorted
        100%
        Library_33_miRNA_mapped_sorted
        100%
        Library_33_piRNA_mapped_sorted
        100%
        Library_33_tRNA_mapped_sorted
        100%
        Library_34
        90.8%
        52%
        29 bp
        10.0
        Library_34_mRNA_mapped_sorted
        100%
        Library_34_miRNA_mapped_sorted
        100%
        Library_34_piRNA_mapped_sorted
        100%
        Library_34_tRNA_mapped_sorted
        100%
        Library_35
        91.6%
        53%
        28 bp
        13.7
        Library_35_mRNA_mapped_sorted
        100%
        Library_35_miRNA_mapped_sorted
        100%
        Library_35_piRNA_mapped_sorted
        100%
        Library_35_tRNA_mapped_sorted
        100%
        Library_36
        85.8%
        52%
        33 bp
        5.8
        Library_36_mRNA_mapped_sorted
        100%
        Library_36_miRNA_mapped_sorted
        100%
        Library_36_piRNA_mapped_sorted
        100%
        Library_36_tRNA_mapped_sorted
        100%
        Library_38
        93.4%
        63%
        33 bp
        35.2
        Library_38_mRNA_mapped_sorted
        100%
        Library_38_miRNA_mapped_sorted
        100%
        Library_38_piRNA_mapped_sorted
        100%
        Library_38_tRNA_mapped_sorted
        100%
        Library_39
        88.7%
        57%
        27 bp
        8.0
        Library_39_mRNA_mapped_sorted
        100%
        Library_39_miRNA_mapped_sorted
        100%
        Library_39_piRNA_mapped_sorted
        100%
        Library_39_tRNA_mapped_sorted
        100%
        Library_40
        87.8%
        57%
        35 bp
        8.2
        Library_40_mRNA_mapped_sorted
        100%
        Library_40_miRNA_mapped_sorted
        100%
        Library_40_piRNA_mapped_sorted
        100%
        Library_40_tRNA_mapped_sorted
        100%

        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Alignment Summary

        Plase note that Picard's read counts are divided by two for paired-end data.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Base Distribution

        Plot shows the distribution of bases by cycle.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        GC Coverage Bias

        This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        loading..

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        loading..

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        loading..

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        loading..

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        loading..

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%